Diet rapidly and reproducibly alters the human gut microbiome

Nature, Journal Year: 2013, Volume and Issue: 505(7484), P. 559 - 563

Published: Dec. 11, 2013

Language: Английский

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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nucleic Acids Research, Journal Year: 2015, Volume and Issue: 44(D1), P. D733 - D745

Published: Nov. 8, 2015

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). leverages data submitted to International Nucleotide Sequence Database Collaboration (INSDC) against combination computation, manual curation, collaboration produce standard set stable, non-redundant reference sequences. augments these sequences with current knowledge including publications, functional features informative nomenclature. currently represents from more than 55 000 organisms (>4800 viruses, >40 prokaryotes >10 eukaryotes; release 71), ranging single record complete genomes. This paper summarizes status viral, prokaryotic, eukaryotic branches project, reports on improvements access details efforts further expand taxonomic representation collection. We also highlight diverse curation initiatives that support multiple uses validation, genome annotation, comparative genomics, clinical testing. summarize our approach utilizing RNA-Seq other types in process vertebrate, plant, species, describe new direction prokaryotic genomes name management.

Language: Английский

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Towards a unified paradigm for sequence‐based identification of fungi

Molecular Ecology, Journal Year: 2013, Volume and Issue: 22(21), P. 5271 - 5277

Published: Aug. 3, 2013

Abstract The nuclear ribosomal internal transcribed spacer ( ITS ) region is the formal fungal barcode and in most cases marker of choice for exploration diversity environmental samples. Two problems are particularly acute pursuit satisfactory taxonomic assignment newly generated sequences: (i) lack an inclusive, reliable public reference data set (ii) means to refer species, which no Latin name available a standardized stable way. Here, we report on progress these regards through further development UNITE database http://unite.ut.ee molecular identification fungi. All species represented by at least two sequences international nucleotide sequence databases now given unique, accession number type (e.g. H ymenoscyphus pseudoalbidus | GU 586904| SH 133781.05 FU ), their ecological annotations were corrected as far possible distributed, third‐party annotation effort. We introduce term ‘species hypothesis’ taxa discovered clustering different similarity thresholds (97–99%). An automatically or manually designated chosen represent each such SH. These released http://unite.ut.ee/repository.php use scientific community in, example, local searches QIIME pipeline. system will be updated grows. invite everybody position improve metadata associated with particular lineages expertise do so new Web‐based management .

Language: Английский

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Global diversity and geography of soil fungi

Science, Journal Year: 2014, Volume and Issue: 346(6213)

Published: Nov. 28, 2014

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds globally distributed soil samples, we demonstrate that richness is decoupled plant diversity. The plant-to-fungus ratio declines exponentially toward poles. Climatic factors, followed by edaphic spatial variables, constitute best predictors community composition at global scale. show similar latitudinal gradients to other organisms, with several notable exceptions. These findings advance our understanding permit integration fungi into a general macroecological framework.

Language: Английский

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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D259 - D264

Published: Oct. 12, 2018

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 public ITS sequences reference. These are clustered into ∼459 species hypotheses assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house third-party curation annotation have resulted in more than 275 improvements data over past 15 years. serves as provider range metabarcoding software pipelines regularly exchanges with major databases other community resources. Recent include redesigned handling unclassifiable hypotheses, integration taxonomic backbone Global Biodiversity Information Facility, support an unlimited number parallel classification systems.

Language: Английский

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The human skin microbiome

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(3), P. 143 - 155

Published: Jan. 15, 2018

Language: Английский

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New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

FEMS Microbiology Ecology, Journal Year: 2012, Volume and Issue: 82(3), P. 666 - 677

Published: June 28, 2012

With recent methodological advances, molecular markers are increasingly used for semi-quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes through PCR places new demands on primers accurately match target sites and provide short amplicons. internal transcribed spacer (ITS) region the ribosome encoding genes is a commonly marker many groups. Here, we describe three - fITS7, gITS7 fITS9, which may be amplify ITS2 by targeting in 5.8S gene. We evaluated compared their performance with ITS1f primer 454-sequencing both artificially assembled templates field samples. When entire ITS was amplified using ITS1f/ITS4 combination, found strong bias against species longer This problem could overcome primers, produce shorter amplicons better composition template. In addition, yielded more diverse amplicon communities than primer.

Language: Английский

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Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

Biological Conservation, Journal Year: 2014, Volume and Issue: 183, P. 4 - 18

Published: Dec. 20, 2014

The continuous decline in Earth's biodiversity represents a major crisis and challenge for the 21st century, there is international political agreement to slow down or halt this decline. large part impeded by lack of knowledge on state distribution – especially since majority species Earth are un-described science. All conservation efforts save essentially depend monitoring populations obtain reliable patterns population size estimates. Such has traditionally relied physical identification visual surveys counting individuals. However, traditional techniques remain problematic due difficulties associated with correct cryptic juvenile life stages, taxonomic expertise, non-standardized sampling, invasive nature some survey techniques. Hence, urgent need alternative efficient large-scale monitoring. Environmental DNA (eDNA) defined here as: genetic material obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs biological source an efficient, non-invasive easy-to-standardize sampling approach. Coupled sensitive, cost-efficient ever-advancing sequencing technology, it may be appropriate candidate been ancient as well modern encompasses single detection analyses ecosystems. research eDNA initiated microbiology, recognizing that culture-based methods grossly misrepresent microbial diversity nature. Subsequently, method assess macro-organismal communities, was first analyzed sediments, revealing extinct extant animals plants, but various terrestrial aquatic samples. Results approaches have provided valuable insights study environments proven useful contemporary In future, we expect eDNA-based move single-marker communities meta-genomic entire ecosystems predict spatial temporal patterns. advances applications range biological, geological sciences. Here review achievements gained through macro-organisms context, discuss its potential advantages limitations

Language: Английский

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NCBI Taxonomy: a comprehensive update on curation, resources and tools

Database, Journal Year: 2020, Volume and Issue: 2020

Published: Jan. 1, 2020

Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications every sequence in the nucleotide protein databases of International Nucleotide Sequence Database Collaboration. Since last review this resource 2012, it has undergone several improvements. Most notable is shift from a single SQL database to series linked tied framework data called NameBank. This means that relations among elements can be adjusted more detail, resulting expanded annotation synonyms, ability flag with specific nomenclatural properties, enhanced tracking publications improved scientific authorities types. Additionally, practices utilized by NCBI curators major taxonomic groups are described, terms peculiar explained, external resources acknowledged updates tools other documented. URL: https://www.ncbi.nlm.nih.gov/taxonomy

Language: Английский

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The Colletotrichum gloeosporioides species complex

Studies in Mycology, Journal Year: 2012, Volume and Issue: 73, P. 115 - 180

Published: Sept. 1, 2012

The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within ITS gene tree. All taxa accepted this are morphologically more or less typical broadly C. gloeosporioides, as it has been applied in literature for past 50 years. We accept 22 plus one subspecies complex. These include asianum, cordylinicola, fructicola, horii, kahawae subsp. kahawae, musae, nupharicola, psidii, siamense, theobromicola, tropicale, and xanthorrhoeae, along with described here new, aenigma, aeschynomenes, alatae, alienum, aotearoa, clidemiae, ciggaro, salsolae, ti, nom. nov. queenslandicum (for var. minus). genetically basis multi-gene phylogenies. Brief morphological descriptions provided where no modern description available. Many unable to be reliably distinguished using ITS, official barcoding fungi. Particularly problematic set close musae another referred Musae Kahawae clade, respectively. Each contains several that phylogenetically well analyses, but clades branch lengths short because small number informative characters, few cases individual trees incongruent. Some single genes combinations genes, such glyceraldehyde-3-phosphate dehydrogenase glutamine synthetase, can used distinguish most will need developed secondary barcodes level identification, which important many these fungi biosecurity significance. In addition species, notes names possible relationship sensu lato suggested recent literature, all subspecific formae speciales its putative teleomorph Glomerella cingulata.

Language: Английский

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